Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 49

System / cell line: real ✕ Assay: validation ✕ Clear

GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.

PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

Has reproduction · 67

GAVISUNK is an open-source pipeline that validates phased diploid HiFi assemblies by assessing concordance of inter-SUNK distances against orthogonal Oxford Nanopore (ONT) reads.

chm13 chm1 hg02723 genome sunk haplotype
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

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Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

cervical independent computational long real-time gene
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

real combined pre-mirna training random independent repeated
Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay.

PMID 18036208 · PMC2253505 · BMC medical genetics · 2007 · 7 claims · 3 setups

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Improved short, non-overlapping TaqMan MGB probes accurately and simultaneously discriminate the H63D, S65C and C282Y HFE polymorphisms without cross-interference between the closely spaced codon 63/65 SNPs.

genomic real-time rflp sequencing
Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

PMID 17324265 · PMC1810516 · BMC medical genetics · 2007 · 8 claims · 3 setups

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Developed a real-time TaqMan PCR method that quantifies PARK2 exon 1-12 copy number by comparing amplification signal to the β-globin internal control gene

genomic same real-time prior
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

pre-mirnas test conserved-hairpin cross-species secondary svm cross-species
Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

PMID 16672055 · PMC1468397 · BMC medical genetics · 2006 · 6 claims · 5 setups

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Molecular beacon-based real-time PCR assays for p.C282Y and p.H63D achieve complete genotype concordance with restriction enzyme digestion and direct sequencing

genomic anonymized dried pcr-restriction direct molecular
Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

zebrafish computational seven consolidated whole-adult-organism supervised quantitative
Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

Has reproduction

Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

duroc 1000-individual real low-coverage genome-wide genomic
Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 7 claims · 6 setups

Has reproduction · 48

The CD8A-high/IDO1-high colon cancer subtype (group IV*) has the worst survival despite high CD8 infiltrates.

tcga-coad ncbi-geo colon c57bl bulk gene immune
RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

PMID 36429012 · PMC9688714 · Cells · 2022 · 6 claims · 7 setups

Has reproduction · 37

RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression.

brain naïve wild-type spinal editing quantitative eae
Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

Has reproduction · 44

The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

spinal brown sci microarray functional protein-protein
All systems GO for understanding mouse gene function.

PMID 15610553 · PMC549721 · Journal of biology · 2004 · 7 claims · 4 setups

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Quantitative, multivariate cross-tissue expression measurements are powerfully predictive of gene function

diverse tissues computational dye-swap reverse-transcription-coupled support
Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach.

PMID 18829526 · PMC2692251 · Cancer research · 2008 · 7 claims · 6 setups

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Global association of HuR and AUF1 with target mRNAs changes substantially and largely reciprocally between MCT-1-transformed and nontransformed MCF10A cells

mcf10a xenograft rip-chip real-time western
Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

prostate subset lncap 22rv1 microrna quantitative western
A genome-wide screen for copy number alterations in Aicardi syndrome.

PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

genomic subject array quantitative fluorescence
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

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BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

reads yoruban cytogenetically predicted simulated paired-end whole-genome
Chips to hits.

PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups

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Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping

individual yeast pools lncap cell-based affymetrix automated
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 7 claims · 4 setups

Has reproduction · 81

CCL8 is a promising independent prognostic factor in DLBCL associated with M2 macrophage interactions

dlbcl ffpe paraffin-embedded bulk quantitative immunofluorescent
Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.

PMID 37810000 · PMC10559070 · Heliyon · 2023 · 7 claims · 7 setups

Has reproduction · 88

SEA and SEB treatment increases proliferation of AML cell lines.

aml cancer proliferation cytotoxicity transwell

Experiments

GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.

Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay.

Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

All systems GO for understanding mouse gene function.

Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach.

Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

A genome-wide screen for copy number alterations in Aicardi syndrome.

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Chips to hits.

CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.